The class LinearHMM is for learning Higher Order Markov chains.
While learning the parameters in
are determined.
A more detailed description can be found in
Durbin et.al, Biological Sequence Analysis -Probabilistic Models of Proteins and Nucleic Acids, 1998
在文件LinearHMM.h第39行定义。
公有成员 | |
CLinearHMM (CStringFeatures< uint16_t > *f) | |
CLinearHMM (int32_t p_num_features, int32_t p_num_symbols) | |
virtual | ~CLinearHMM () |
virtual bool | train (CFeatures *data=NULL) |
bool | train (const int32_t *indizes, int32_t num_indizes, float64_t pseudo_count) |
float64_t | get_log_likelihood_example (uint16_t *vector, int32_t len) |
float64_t | get_likelihood_example (uint16_t *vector, int32_t len) |
virtual float64_t | get_log_likelihood_example (int32_t num_example) |
virtual float64_t | get_log_derivative (int32_t num_param, int32_t num_example) |
virtual float64_t | get_log_derivative_obsolete (uint16_t obs, int32_t pos) |
virtual float64_t | get_derivative_obsolete (uint16_t *vector, int32_t len, int32_t pos) |
virtual int32_t | get_sequence_length () |
virtual int32_t | get_num_symbols () |
virtual int32_t | get_num_model_parameters () |
virtual float64_t | get_positional_log_parameter (uint16_t obs, int32_t position) |
virtual float64_t | get_log_model_parameter (int32_t num_param) |
virtual void | get_log_transition_probs (float64_t **dst, int32_t *num) |
virtual bool | set_log_transition_probs (const float64_t *src, int32_t num) |
virtual void | get_transition_probs (float64_t **dst, int32_t *num) |
virtual bool | set_transition_probs (const float64_t *src, int32_t num) |
virtual const char * | get_name () const |
保护属性 | |
int32_t | sequence_length |
int32_t | num_symbols |
int32_t | num_params |
float64_t * | transition_probs |
float64_t * | log_transition_probs |
CLinearHMM | ( | CStringFeatures< uint16_t > * | f | ) |
CLinearHMM | ( | int32_t | p_num_features, | |
int32_t | p_num_symbols | |||
) |
constructor
p_num_features | number of features | |
p_num_symbols | number of symbols in features |
在文件LinearHMM.cpp第28行定义。
~CLinearHMM | ( | ) | [virtual] |
在文件LinearHMM.cpp第36行定义。
virtual float64_t get_derivative_obsolete | ( | uint16_t * | vector, | |
int32_t | len, | |||
int32_t | pos | |||
) | [virtual] |
obsolete get one example's derivative
vector | vector | |
len | length | |
pos | position |
在文件LinearHMM.h第127行定义。
float64_t get_likelihood_example | ( | uint16_t * | vector, | |
int32_t | len | |||
) |
get one example's likelihood
vector | the example | |
len | length of vector |
在文件LinearHMM.cpp第201行定义。
float64_t get_log_derivative | ( | int32_t | num_param, | |
int32_t | num_example | |||
) | [virtual] |
get logarithm of one example's derivative's likelihood
num_param | which example's param | |
num_example | which example |
实现了CDistribution。
在文件LinearHMM.cpp第211行定义。
virtual float64_t get_log_derivative_obsolete | ( | uint16_t | obs, | |
int32_t | pos | |||
) | [virtual] |
obsolete get logarithm of one example's derivative's likelihood
obs | observation | |
pos | position |
在文件LinearHMM.h第115行定义。
float64_t get_log_likelihood_example | ( | int32_t | num_example | ) | [virtual] |
get logarithm of one example's likelihood
num_example | which example |
实现了CDistribution。
在文件LinearHMM.cpp第184行定义。
float64_t get_log_likelihood_example | ( | uint16_t * | vector, | |
int32_t | len | |||
) |
get logarithm of one example's likelihood
vector | the example | |
len | length of vector |
在文件LinearHMM.cpp第174行定义。
virtual float64_t get_log_model_parameter | ( | int32_t | num_param | ) | [virtual] |
get logarithm of given model parameter
num_param | which param |
实现了CDistribution。
在文件LinearHMM.h第169行定义。
void get_log_transition_probs | ( | float64_t ** | dst, | |
int32_t * | num | |||
) | [virtual] |
get logarithm of all transition probs
dst | where logarithm of transition probs will be stored | |
num | where number of logarithm of transition probs will be stored |
在文件LinearHMM.cpp第260行定义。
virtual const char* get_name | ( | ) | const [virtual] |
virtual int32_t get_num_model_parameters | ( | ) | [virtual] |
get number of model parameters
实现了CDistribution。
在文件LinearHMM.h第150行定义。
virtual int32_t get_num_symbols | ( | ) | [virtual] |
virtual float64_t get_positional_log_parameter | ( | uint16_t | obs, | |
int32_t | position | |||
) | [virtual] |
get positional log parameter
obs | observation | |
position | position |
在文件LinearHMM.h第158行定义。
virtual int32_t get_sequence_length | ( | ) | [virtual] |
void get_transition_probs | ( | float64_t ** | dst, | |
int32_t * | num | |||
) | [virtual] |
get all transition probs
dst | where transition probs will be stored | |
num | where number of transition probs will be stored |
在文件LinearHMM.cpp第230行定义。
bool set_log_transition_probs | ( | const float64_t * | src, | |
int32_t | num | |||
) | [virtual] |
set logarithm of all transition probs
src | new logarithms of transition probs | |
num | number of logarithms of transition probs |
在文件LinearHMM.cpp第270行定义。
bool set_transition_probs | ( | const float64_t * | src, | |
int32_t | num | |||
) | [virtual] |
set all transition probs
src | new transition probs | |
num | number of transition probs |
在文件LinearHMM.cpp第240行定义。
bool train | ( | const int32_t * | indizes, | |
int32_t | num_indizes, | |||
float64_t | pseudo_count | |||
) |
alternative train distribution
indizes | indices | |
num_indizes | number of indices | |
pseudo_count | pseudo count |
在文件LinearHMM.cpp第111行定义。
bool train | ( | CFeatures * | data = NULL |
) | [virtual] |
estimate LinearHMM distribution
data | training data (parameter can be avoided if distance or kernel-based classifiers are used and distance/kernels are initialized with train data) |
实现了CDistribution。
在文件LinearHMM.cpp第42行定义。
float64_t* log_transition_probs [protected] |
logarithm of transition probs
在文件LinearHMM.h第223行定义。
int32_t num_params [protected] |
number of parameters
在文件LinearHMM.h第219行定义。
int32_t num_symbols [protected] |
number of symbols in examples
在文件LinearHMM.h第217行定义。
int32_t sequence_length [protected] |
examples' sequence length
在文件LinearHMM.h第215行定义。
float64_t* transition_probs [protected] |
transition probs
在文件LinearHMM.h第221行定义。